1
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Feng Y, Roos WH. Atomic Force Microscopy: An Introduction. Methods Mol Biol 2024; 2694:295-316. [PMID: 37824010 DOI: 10.1007/978-1-0716-3377-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields, for instance, in biological sciences, where it is paramount to investigate structures at the single particle level. Often, two-dimensional images are not sufficient, and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. New developments in AFM are discussed, and by including approaches such as bimodal AFM and high-speed AFM (HS-AFM), we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
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Affiliation(s)
- Yuzhen Feng
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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2
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Gisbert VG, Garcia R. Insights and guidelines to interpret forces and deformations at the nanoscale by using a tapping mode AFM simulator: dForce 2.0. SOFT MATTER 2023; 19:5857-5868. [PMID: 37305960 DOI: 10.1039/d3sm00334e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Amplitude modulation (tapping mode) AFM is the most versatile AFM mode for imaging surfaces at the nanoscale in air and liquid environments. However, it remains challenging to estimate the forces and deformations exerted by the tip. We introduce a new simulator environment to predict the values of the observables in tapping mode AFM experiments. The relevant feature of dForce 2.0 is the incorporation of contact mechanics models aimed to describe the properties of ultrathin samples. These models were essential to determine the forces applied on samples such as proteins, self-assembled monolayers, lipid bilayers, and few-layered materials. The simulator incorporates two types of long-range magnetic forces. The simulator is written in an open-source code (Python) and it can be run from a personal computer.
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Affiliation(s)
- Victor G Gisbert
- Instituto de Ciencia de Materiales de Madrid, CSIC c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
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3
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Irvin EM, Wang H. Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures. DNA Repair (Amst) 2023; 128:103528. [PMID: 37392578 PMCID: PMC10989508 DOI: 10.1016/j.dnarep.2023.103528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
DNA repair pathways are tightly regulated processes that recognize specific hallmarks of DNA damage and coordinate lesion repair through discrete mechanisms, all within the context of a three-dimensional chromatin landscape. Dysregulation or malfunction of any one of the protein constituents in these pathways can contribute to aging and a variety of diseases. While the collective action of these many proteins is what drives DNA repair on the organismal scale, it is the interactions between individual proteins and DNA that facilitate each step of these pathways. In much the same way that ensemble biochemical techniques have characterized the various steps of DNA repair pathways, single-molecule imaging (SMI) approaches zoom in further, characterizing the individual protein-DNA interactions that compose each pathway step. SMI techniques offer the high resolving power needed to characterize the molecular structure and functional dynamics of individual biological interactions on the nanoscale. In this review, we highlight how our lab has used SMI techniques - traditional atomic force microscopy (AFM) imaging in air, high-speed AFM (HS-AFM) in liquids, and the DNA tightrope assay - over the past decade to study protein-nucleic acid interactions involved in DNA repair, mitochondrial DNA replication, and telomere maintenance. We discuss how DNA substrates containing specific DNA sequences or structures that emulate DNA repair intermediates or telomeres were generated and validated. For each highlighted project, we discuss novel findings made possible by the spatial and temporal resolution offered by these SMI techniques and unique DNA substrates.
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Affiliation(s)
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, NC, USA; Physics Department, North Carolina State University, Raleigh, NC, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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4
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Lu N, Xiao S, Zhang R, Liu J, Ma L, Wu S. Thin head atomic force microscope for integration with optical microscope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:083702. [PMID: 36050041 DOI: 10.1063/5.0093080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
We present a novel thin head atomic force microscope (AFM) that can be easily integrated with an upright optical microscope (OM). The optical beam detection unit in the AFM used an obliquely incident laser beam onto the cantilever, reducing the AFM head's effective thickness to 7.3 mm. That allows an open space above the cantilever probe to accommodate the objective lens up to 0.6 numerical aperture (N.A.) without obstruction. A multi-function digital controller was developed to control the AFM and reserved interfaces to communicate with the OM. To assess the performance of the developed AFM, we first measured the noise level and bandwidths of the AFM system. Then, the imaging quality of the AFM was evaluated by both calibration grids and two-dimensional materials. Finally, the thin head AFM was integrated into a homemade white light interferometer as a demonstration of combined use with an advanced optical system. The experimental results demonstrated that our developed AFM is suitable for integration under upright OM and brings AFM high-resolution advantages to the existing OM system.
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Affiliation(s)
- Nianhang Lu
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Shasha Xiao
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Rui Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Jirui Liu
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Long Ma
- Sino-European Institute of Aviation Engineering, Civil Aviation University of China, Tianjin 300300, China
| | - Sen Wu
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China
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5
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Gachon E, Mesquida P. Mechanical properties of collagen fibrils determined by buckling analysis. Acta Biomater 2022; 149:60-68. [PMID: 35803503 DOI: 10.1016/j.actbio.2022.06.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022]
Abstract
The mechanical properties of biological nanofibers such as collagen fibrils are important in many applications, ranging from tissue-engineering to cancer treatment. However, mechanical testing is not straightforward at the nanometer scale. Here, we use the theory of column-buckling to determine the bending properties of individual collagen fibrils. To achieve this, fibrils were deposited on a manually pre-stretched foil, which was then released with the fibrils attached. Atomic Force Microscopy (AFM) imaging was used to determine the tensile modulus by measuring the buckling-wavelength and the radius for each fibril. Comparison with data obtained by AFM nanoindentation and other, more sophisticated methods, shows that our results are in very good agreement. The great advantage of this simple approach is that it can be used to quickly determine mechanical properties without force or stress-strain measurements, which are challenging to obtain accurately and at high throughput at the nanoscale. The method could be applied to any nanofibers, not just collagen fibrils. STATEMENT OF SIGNIFICANCE: Collagen fibrils are the main constituent of the extracellular matrix, and alterations of their mechanical properties can have significant effects on cell adhesion and motility. This has, ultimately, implications in age-related diseases and cancer. Furthermore, tuning the mechanical properties of collagen fibrils could be an important tool in the design of artificial cell scaffolds in tissue-engineering. For these reasons, it is important to have methods that can be used to determine the mechanical properties of fibrils at the single-fibril level and, therefore, at the nanometer scale. The method presented here has the advantage of being easy to use and avoids some of the fundamental issues of more established methods.
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Affiliation(s)
- Emilie Gachon
- Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Patrick Mesquida
- Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom.
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6
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Ngo KX, Nguyen PDN, Furusho H, Miyata M, Shimonaka T, Chau NNB, Vinh NP, Nghia NA, Mohammed TO, Ichikawa T, Kodera N, Konno H, Fukuma T, Quoc NB. Unraveling the Host-Selective Toxic Interaction of Cassiicolin with Lipid Membranes and Its Cytotoxicity. PHYTOPATHOLOGY 2022; 112:1524-1536. [PMID: 35238604 DOI: 10.1094/phyto-09-21-0397-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cassiicolin (Cas), a toxin produced by Corynespora cassiicola, is responsible for Corynespora leaf fall disease in susceptible rubber trees. Currently, the molecular mechanisms of the cytotoxicity of Cas and its host selectivity have not been fully elucidated. Here, we analyzed the binding of Cas1 and Cas2 to membranes consisting of different plant lipids and their membrane disruption activities. Using high-speed atomic force microscopy and confocal microscopy, we reveal that the binding and disruption activities of Cas1 and Cas2 on lipid membranes are strongly dependent on the specific plant lipids. The negative phospholipids, glycerolipids, and sterols are more sensitive to membrane damage caused by Cas1 and Cas2 than neutral phospholipids and betaine lipids. Mature Cas1 and Cas2 play an essential role in causing membrane disruption. Cytotoxicity tests on rubber leaves of Rubber Research Institute of Vietnam (RRIV) 1, RRIV 4, and Prang Besar (PB) 255 clones suggest that the toxins cause necrosis of rubber leaves, except for the strong resistance of PB 255 against Cas2. Cryogenic scanning electron microscopy analyses of necrotic leaf tissues treated with Cas1 confirm that cytoplasmic membranes are vulnerable to the toxin. Thus, the host selectivity of Cas toxin is attained by the lipid-dependent binding activity of Cas to the membrane, and the cytotoxicity of Cas arises from its ability to form biofilm-like structures and to disrupt specific membranes.
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Affiliation(s)
- Kien Xuan Ngo
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Phuong Doan N Nguyen
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
- Research Institute for Biotechnology and Environment, Nong Lam University, Ho Chi Minh City, Vietnam
| | - Hirotoshi Furusho
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Tomomi Shimonaka
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Nguyen Ngoc Bao Chau
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam
| | | | | | - Tareg Omer Mohammed
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Takehiko Ichikawa
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Hiroki Konno
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Takeshi Fukuma
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Nguyen Bao Quoc
- Research Institute for Biotechnology and Environment, Nong Lam University, Ho Chi Minh City, Vietnam
- Faculty of Biological Sciences, Nong Lam University, Ho Chi Minh City, Vietnam
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7
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Tsudome M, Tachioka M, Miyazaki M, Uchimura K, Tsuda M, Takaki Y, Deguchi S. An ultrasensitive nanofiber-based assay for enzymatic hydrolysis and deep-sea microbial degradation of cellulose. iScience 2022; 25:104732. [PMID: 36039358 PMCID: PMC9418596 DOI: 10.1016/j.isci.2022.104732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/10/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mikiko Tsudome
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Mikako Tachioka
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masayuki Miyazaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kohsuke Uchimura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Miwako Tsuda
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Takaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Corresponding author
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8
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Review on the applications of atomic force microscopy imaging in proteins. Micron 2022; 159:103293. [DOI: 10.1016/j.micron.2022.103293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022]
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9
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Murphy JG, Raybin JG, Sibener SJ. Correlating polymer structure, dynamics, and function with atomic force microscopy. JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1002/pol.20210321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julia G. Murphy
- The James Franck Institute and Department of Chemistry The University of Chicago Chicago Illinois USA
| | - Jonathan G. Raybin
- The James Franck Institute and Department of Chemistry The University of Chicago Chicago Illinois USA
| | - Steven J. Sibener
- The James Franck Institute and Department of Chemistry The University of Chicago Chicago Illinois USA
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10
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Fang B, Zhao L, Du X, Liu Q, Yang H, Li F, Sheng Y, Zhao W, Zhong H. Studying the
Rhodopsin‐Like
G Protein Coupled Receptors by Atomic Force Microscopy. Cytoskeleton (Hoboken) 2022; 78:400-416. [DOI: 10.1002/cm.21692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Bin Fang
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Li Zhao
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Xiaowei Du
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Qiyuan Liu
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
- School of Basic Medicine Gannan Medical University Ganzhou People's Republic of China
| | - Hui Yang
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Fangzuo Li
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Yaohuan Sheng
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Weidong Zhao
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
| | - Haijian Zhong
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province Gannan Medical University Ganzhou People's Republic of China
- School of Medical Information Engineering Gannan Medical University Ganzhou People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education Gannan Medical University Ganzhou People's Republic of China
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11
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Moreira RA, Baker JL, Guzman HV, Poma AB. Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations. Methods Mol Biol 2022; 2340:357-378. [PMID: 35167082 DOI: 10.1007/978-1-0716-1546-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The nanomechanical characterization of several biological fibrils that are the result of protein aggregation via molecular dynamics simulation is nowadays feasible, and together with atomic force microscopy experiments has widened our understanding of the forces in the regime of pN-nN and system sizes of about hundreds of nanometers. Several methodologies have been developed to achieve this target, and they range from the atomistic representation via molecular force fields to coarse-grained strategies that provide comparable results with experiments in a systematic way. In this chapter, we discuss several methodologies for the calculation of mechanical parameters, such as the elastic constants of relevant biological systems. They are presented together with details about parameterization and current limitations. Then, we discuss some of the applications of such methodologies for the description of bacterial filament and β-amyloid systems. Finally, the latest lines of development are discussed.
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Affiliation(s)
- Rodrigo A Moreira
- Soft Matter and Biosystems, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Joseph L Baker
- Department of Chemistry, The College of New Jersey, Ewing, NJ, USA
| | | | - Adolfo B Poma
- Soft Matter and Biosystems, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland.
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12
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Abstract
In the scanning probe microscope system, the weak signal detection of cantilever vibration is one of the important factors affecting the sensor sensitivity. In our current work, we present a novel design concept for an atomic force microscope (AFM) combined with optomechanics with an ultra-high quality factor and a low thermal noise. The detection system consists of a fixed mirror placed on the cantilever of the AFM and pump-probe beams that is equivalent to a Fabry-Perot cavity. We realize that the AFM combined with an optical cavity can achieve ultra-sensitive detection of force gradients of 10-12 N m-1 in the case of high-vacuum and low effective temperature of 1 mK, which may open up new avenues for super-high resolution imaging and super-high precision force spectroscopy.
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Affiliation(s)
- Fei He
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Jian Liu
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Ka-Di Zhu
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
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13
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Miranda A, Gómez-Varela AI, Stylianou A, Hirvonen LM, Sánchez H, De Beule PAA. How did correlative atomic force microscopy and super-resolution microscopy evolve in the quest for unravelling enigmas in biology? NANOSCALE 2021; 13:2082-2099. [PMID: 33346312 DOI: 10.1039/d0nr07203f] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the invention of the Atomic Force Microscope (AFM) in 1986 and the subsequent developments in liquid imaging and cellular imaging it became possible to study the topography of cellular specimens under nearly physiological conditions with nanometric resolution. The application of AFM to biological research was further expanded with the technological advances in imaging modes where topographical data can be combined with nanomechanical measurements, offering the possibility to retrieve the biophysical properties of tissues, cells, fibrous components and biomolecules. Meanwhile, the quest for breaking the Abbe diffraction limit restricting microscopic resolution led to the development of super-resolution fluorescence microscopy techniques that brought the resolution of the light microscope comparable to the resolution obtained by AFM. The instrumental combination of AFM and optical microscopy techniques has evolved over the last decades from integration of AFM with bright-field and phase-contrast imaging techniques at first to correlative AFM and wide-field fluorescence systems and then further to the combination of AFM and fluorescence based super-resolution microscopy modalities. Motivated by the many developments made over the last decade, we provide here a review on AFM combined with super-resolution fluorescence microscopy techniques and how they can be applied for expanding our understanding of biological processes.
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Affiliation(s)
- Adelaide Miranda
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
| | - Ana I Gómez-Varela
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal. and Department of Applied Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain.
| | - Andreas Stylianou
- Cancer Biophysics Laboratory, University of Cyprus, Nicosia, Cyprus and School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Liisa M Hirvonen
- Centre for Microscopy, Characterisation and Analysis (CMCA), The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Humberto Sánchez
- Faculty of Applied Sciences, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Pieter A A De Beule
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
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14
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Manickavasagam AK, Gutschmidt S, Sellier M. Hydrodynamic loading profiles of viscously-interacting blocks subject to different stimulus locations. J R Soc N Z 2021. [DOI: 10.1080/03036758.2020.1857802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Arun K. Manickavasagam
- Department of Mechanical Engineering, University of Canterbury, Christchurch, New Zealand
| | - Stefanie Gutschmidt
- Department of Mechanical Engineering, University of Canterbury, Christchurch, New Zealand
| | - Mathieu Sellier
- Department of Mechanical Engineering, University of Canterbury, Christchurch, New Zealand
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15
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Farokh Payam A, Biglarbeigi P, Morelli A, Lemoine P, McLaughlin J, Finlay D. Data acquisition and imaging using wavelet transform: a new path for high speed transient force microscopy. NANOSCALE ADVANCES 2021; 3:383-398. [PMID: 36131753 PMCID: PMC9417248 DOI: 10.1039/d0na00531b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/10/2020] [Indexed: 06/13/2023]
Abstract
The unique ability of Atomic Force Microscopy (AFM) to image, manipulate and characterize materials at the nanoscale has made it a remarkable tool in nanotechnology. In dynamic AFM, acquisition and processing of the photodetector signal originating from probe-sample interaction is a critical step in data analysis and measurements. However, details of such interaction including its nonlinearity and dynamics of the sample surface are limited due to the ultimately bounded bandwidth and limited time scales of data processing electronics of standard AFM. Similarly, transient details of the AFM probe's cantilever signal are lost due to averaging of data by techniques which correlate the frequency spectrum of the captured data with a temporally invariant physical system. Here, we introduce a fundamentally new approach for dynamic AFM data acquisition and imaging based on applying the wavelet transform on the data stream from the photodetector. This approach provides the opportunity for exploration of the transient response of the cantilever, analysis and imaging of the dynamics of amplitude and phase of the signals captured from the photodetector. Furthermore, it can be used for the control of AFM which would yield increased imaging speed. Hence the proposed method opens a pathway for high-speed transient force microscopy.
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Affiliation(s)
- Amir Farokh Payam
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University Jordanstown Shore Road Northern Ireland BT37 0QB UK
| | - Pardis Biglarbeigi
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University Jordanstown Shore Road Northern Ireland BT37 0QB UK
| | - Alessio Morelli
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University Jordanstown Shore Road Northern Ireland BT37 0QB UK
| | - Patrick Lemoine
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University Jordanstown Shore Road Northern Ireland BT37 0QB UK
| | - James McLaughlin
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University Jordanstown Shore Road Northern Ireland BT37 0QB UK
| | - Dewar Finlay
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University Jordanstown Shore Road Northern Ireland BT37 0QB UK
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16
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Gisbert V, Benaglia S, Uhlig MR, Proksch R, Garcia R. High-Speed Nanomechanical Mapping of the Early Stages of Collagen Growth by Bimodal Force Microscopy. ACS NANO 2021; 15:1850-1857. [PMID: 33412008 PMCID: PMC8477367 DOI: 10.1021/acsnano.0c10159] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/05/2021] [Indexed: 05/07/2023]
Abstract
High-speed atomic force microscopy (AFM) enabled the imaging of protein interactions with millisecond time resolutions (10 fps). However, the acquisition of nanomechanical maps of proteins is about 100 times slower. Here, we developed a high-speed bimodal AFM that provided high-spatial resolution maps of the elastic modulus, the loss tangent, and the topography at imaging rates of 5 fps. The microscope was applied to identify the initial stages of the self-assembly of the collagen structures. By following the changes in the physical properties, we identified four stages, nucleation and growth of collagen precursors, formation of tropocollagen molecules, assembly of tropocollagens into microfibrils, and alignment of microfibrils to generate microribbons. Some emerging collagen structures never matured, and after an existence of several seconds, they disappeared into the solution. The elastic modulus of a microfibril (∼4 MPa) implied very small stiffness (∼3 × 10-6 N/m). Those values amplified the amplitude of the collagen thermal fluctuations on the mica plane, which facilitated microribbon build-up.
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Affiliation(s)
- Victor
G. Gisbert
- Instituto
de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Simone Benaglia
- Instituto
de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Manuel R. Uhlig
- Instituto
de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Roger Proksch
- Asylum
Research an Oxford Instruments Company, Santa Barbara, California 93117, United States
| | - Ricardo Garcia
- Instituto
de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
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17
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Casuso I, Redondo-Morata L, Rico F. Biological physics by high-speed atomic force microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190604. [PMID: 33100165 PMCID: PMC7661283 DOI: 10.1098/rsta.2019.0604] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
While many fields have contributed to biological physics, nanotechnology offers a new scale of observation. High-speed atomic force microscopy (HS-AFM) provides nanometre structural information and dynamics with subsecond resolution of biological systems. Moreover, HS-AFM allows us to measure piconewton forces within microseconds giving access to unexplored, fast biophysical processes. Thus, HS-AFM provides a tool to nourish biological physics through the observation of emergent physical phenomena in biological systems. In this review, we present an overview of the contribution of HS-AFM, both in imaging and force spectroscopy modes, to the field of biological physics. We focus on examples in which HS-AFM observations on membrane remodelling, molecular motors or the unfolding of proteins have stimulated the development of novel theories or the emergence of new concepts. We finally provide expected applications and developments of HS-AFM that we believe will continue contributing to our understanding of nature, by serving to the dialogue between biology and physics. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.
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Affiliation(s)
- Ignacio Casuso
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
| | - Lorena Redondo-Morata
- Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, 59000 Lille, France
| | - Felix Rico
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
- e-mail:
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18
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Garcia R. Nanomechanical mapping of soft materials with the atomic force microscope: methods, theory and applications. Chem Soc Rev 2020; 49:5850-5884. [PMID: 32662499 DOI: 10.1039/d0cs00318b] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Fast, high-resolution, non-destructive and quantitative characterization methods are needed to develop materials with tailored properties at the nanoscale or to understand the relationship between mechanical properties and cell physiology. This review introduces the state-of-the-art force microscope-based methods to map at high-spatial resolution the elastic and viscoelastic properties of soft materials. The experimental methods are explained in terms of the theories that enable the transformation of observables into material properties. Several applications in materials science, molecular biology and mechanobiology illustrate the scope, impact and potential of nanomechanical mapping methods.
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Affiliation(s)
- Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
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19
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Kodera N, Ando T. High-Speed Atomic Force Microscopy to Study Myosin Motility. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1239:127-152. [PMID: 32451858 DOI: 10.1007/978-3-030-38062-5_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
High-speed atomic force microscopy (HS-AFM) is a unique tool that enables imaging of protein molecules during their functional activity at sub-100 ms temporal and submolecular spatial resolution. HS-AFM is suited for the study of highly dynamic proteins, including myosin motors. HS-AFM images of myosin V walking on actin filaments provide irrefutable evidence for the swinging lever arm motion propelling the molecule forward. Moreover, molecular behaviors that have not been noticed before are also displayed on the AFM movies. This chapter describes the principle, underlying techniques and performance of HS-AFM, filmed images of myosin V, and mechanistic insights into myosin motility provided from the filmed images.
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Affiliation(s)
- Noriyuki Kodera
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kanazawa, Japan.
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20
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Garcia PD, Guerrero CR, Garcia R. Nanorheology of living cells measured by AFM-based force-distance curves. NANOSCALE 2020; 12:9133-9143. [PMID: 32293616 DOI: 10.1039/c9nr10316c] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Mechanobiology aims to establish functional relationships between the mechanical state of a living a cell and its physiology. The acquisition of force-distance curves with an AFM is by far the dominant method to characterize the nanomechanical properties of living cells. However, theoretical simulations have shown that the contact mechanics models used to determine the Young's modulus from a force-distance curve could be off by a factor 5 from its expected value. The semi-quantitative character arises from the lack of a theory that integrates the AFM data, a realistic viscoelastic model of a cell and its finite-thickness. Here, we develop a method to determine the mechanical response of a cell from a force-distance curve. The method incorporates bottom-effect corrections, a power-law rheology model and the deformation history of the cell. It transforms the experimental data into viscoelastic parameters of the cell as a function of the indentation frequency. The quantitative agreement obtained between the experiments performed on living fibroblast cells and the analytical theory supports the use of force-distance curves to measure the nanorheological properties of cells.
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Affiliation(s)
- Pablo D Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
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21
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Synchronous, Crosstalk-free Correlative AFM and Confocal Microscopies/Spectroscopies. Sci Rep 2020; 10:7098. [PMID: 32341407 PMCID: PMC7184616 DOI: 10.1038/s41598-020-62529-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/14/2020] [Indexed: 11/08/2022] Open
Abstract
Microscopies have become pillars of our characterization tools to observe biological systems and assemblies. Correlative and synchronous use of different microscopies relies on the fundamental assumption of non-interference during images acquisitions. In this work, by exploring the correlative use of Atomic Force Microscopy and confocal-Fluorescence-Lifetime Imaging Microscopy (AFM-FLIM), we quantify cross-talk effects occurring during synchronous acquisition. We characterize and minimize optomechanical forces on different AFM cantilevers interfering with normal AFM operation as well as spurious luminescence from the tip and cantilever affecting time-resolved fluorescence detection. By defining non-interfering experimental imaging parameters, we show accurate real-time acquisition and two-dimensional mapping of interaction force, fluorescence lifetime and intensity characterizing morphology (AFM) and local viscosity (FLIM) of gel and fluid phases separation of supported lipid model membranes. Finally, as proof of principle by means of synchronous force and fluorescence spectroscopies, we precisely tune the lifetime of a fluorescent nanodiamond positioned on the AFM tip by controlling its distance from a metallic surface. This opens up a novel pathway of quench sensing to image soft biological samples such as membranes since it does not require tip-sample mechanical contact in contrast with conventional AFM in liquid.
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22
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Srivastava A, Tiwari SP, Miyashita O, Tama F. Integrative/Hybrid Modeling Approaches for Studying Biomolecules. J Mol Biol 2020; 432:2846-2860. [DOI: 10.1016/j.jmb.2020.01.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
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23
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Bio-assay of Acintobacter baumannii using DNA conjugated with gold nano-star: A new platform for microorganism analysis. Enzyme Microb Technol 2020; 133:109466. [PMID: 31874682 DOI: 10.1016/j.enzmictec.2019.109466] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 11/18/2022]
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24
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Niina T, Fuchigami S, Takada S. Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations. J Chem Theory Comput 2020; 16:1349-1358. [PMID: 31909999 DOI: 10.1021/acs.jctc.9b00991] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High-speed (HS) atomic force microscopy (AFM) is a prominent imaging technology that observes large-scale structural dynamics of biomolecules near the physiological condition, but the AFM data are limited to the surface shape of specimens. Rigid-body fitting methods were developed to obtain molecular structures that fit to an AFM image, without accounting for conformational changes. Here, we developed a method to fit flexibly a three-dimensional (3D) biomolecular structure into an AFM image. First, we describe a method to produce a pseudo-AFM image from a given 3D structure in a differentiable form. Then, using a correlation function between the experimental AFM image and the computational pseudo-AFM image, we developed a flexible fitting molecular dynamics (MD) simulation method by which we obtain protein structures that well fit to the given AFM image. We first test it with a twin experiment; using an AFM image produced from a protein structure different from its native conformation as a reference, we performed the flexible fitting MD simulations to sample conformations that fit well the reference AFM image, and the method was confirmed to work well. Then, parameter dependence in the protocol was discussed. Finally, we applied the method to a real experimental HS-AFM image for a flagellar protein FlhA, demonstrating its applicability. We also test the rigid-body fitting of a molecular structure to an AFM image. Our method will be a general tool for dynamic structure modeling based on HS-AFM images and is publicly available through the CafeMol software.
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Affiliation(s)
- Toru Niina
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | - Sotaro Fuchigami
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
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25
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Yilmaz N, Kodama Y, Numata K. Revealing the Architecture of the Cell Wall in Living Plant Cells by Bioimaging and Enzymatic Degradation. Biomacromolecules 2020; 21:95-103. [PMID: 31496226 DOI: 10.1021/acs.biomac.9b00979] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Plant cell walls consist mostly of crystalline cellulose fibrils embedded in a matrix of complex polysaccharides, but information on their morphological features has generally been limited to that obtained from nonliving plant specimens. Here, we characterized the primary cell wall of a living plant cell (from the tobacco BY-2 suspension culture) at nanometer resolution using high-speed atomic force microscopy and at micrometer resolution using confocal laser scanning microscopy. Our results showed aligned and disordered cellulose fibrils coexisting in the outermost layer of the cell wall. We investigated the orientation of the aligned cellulose fibrils in the outer lamellae of the cell wall of living plant cells after removing cellulose, hemicellulose, and pectin by enzymatic degradation to make the cellulose fibrils more visible and, accordingly, to reveal the structure of the nanoachitecture formed by these fibrils within the cell wall. We observed that the cellulose fibrils in the outermost layer were usually oriented close to the direction of cell growth, whereas the orientation of the cellulose fibrils in the successive lamellae further inward changed randomly. Such organization should be crucial to render the plant cell wall both rigid and flexible. This finding provides insight not only into the structure of the functional plant cell wall but also into its growth mechanism.
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Affiliation(s)
- Neval Yilmaz
- Biomacromolecules Research Team , RIKEN Center for Sustainable Resource Science , Wako , Saitama , Japan
| | - Yutaka Kodama
- Biomacromolecules Research Team , RIKEN Center for Sustainable Resource Science , Wako , Saitama , Japan
- Center for Bioscience Research and Education , Utsunomiya University , Tochigi , Japan
| | - Keiji Numata
- Biomacromolecules Research Team , RIKEN Center for Sustainable Resource Science , Wako , Saitama , Japan
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26
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Harcombe DM, Ruppert MG, Fleming AJ. A review of demodulation techniques for multifrequency atomic force microscopy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:76-91. [PMID: 31976199 PMCID: PMC6964647 DOI: 10.3762/bjnano.11.8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/11/2019] [Indexed: 05/29/2023]
Abstract
This article compares the performance of traditional and recently proposed demodulators for multifrequency atomic force microscopy. The compared methods include the lock-in amplifier, coherent demodulator, Kalman filter, Lyapunov filter, and direct-design demodulator. Each method is implemented on a field-programmable gate array (FPGA) with a sampling rate of 1.5 MHz. The metrics for comparison include the sensitivity to other frequency components and the magnitude of demodulation artifacts for a range of demodulator bandwidths. Performance differences are demonstrated through higher harmonic atomic force microscopy imaging.
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Affiliation(s)
- David M Harcombe
- School of Electrical Engineering and Computing, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Michael G Ruppert
- School of Electrical Engineering and Computing, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Andrew J Fleming
- School of Electrical Engineering and Computing, The University of Newcastle, Callaghan, NSW, 2308, Australia
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27
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Dasgupta B, Miyashita O, Tama F. Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images. Biochim Biophys Acta Gen Subj 2019; 1864:129420. [PMID: 31472175 DOI: 10.1016/j.bbagen.2019.129420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Atomic Force Microscopy (AFM) is an experimental technique to study structure-function relationship of biomolecules. AFM provides images of biomolecules at nanometer resolution. High-speed AFM experiments produce a series of images following dynamics of biomolecules. To further understand biomolecular functions, information on three-dimensional (3D) structures is beneficial. METHOD We aim to recover 3D information from an AFM image by computational modeling. The AFM image includes only low-resolution representation of a molecule; therefore we represent the structures by a coarse grained model (Gaussian mixture model). Using Monte-Carlo sampling, candidate models are generated to increase similarity between AFM images simulated from the models and target AFM image. RESULTS The algorithm was tested on two proteins to model their conformational transitions. Using a simulated AFM image as reference, the algorithm can produce a low-resolution 3D model of the target molecule. Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that similar accuracy can be obtained for many orientations. CONCLUSIONS The proposed algorithm can generate 3D low-resolution protein models, from which conformational transitions observed in AFM images can be interpreted in more detail. GENERAL SIGNIFICANCE High-speed AFM experiments allow us to directly observe biomolecules in action, which provides insights on biomolecular function through dynamics. However, as only partial structural information can be obtained from AFM data, this new AFM based hybrid modeling method would be useful to retrieve 3D information of the entire biomolecule.
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Affiliation(s)
- Bhaskar Dasgupta
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Osamu Miyashita
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Florence Tama
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan; Department of Physics, Graduate School of Science, Nagoya University, Aichi, 464-8602, Japan; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, 464-8601, Japan.
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29
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Ando T. High-speed atomic force microscopy. Curr Opin Chem Biol 2019; 51:105-112. [DOI: 10.1016/j.cbpa.2019.05.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
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30
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Xia A, Yang S, Zhang R, Ni L, Xing X, Jin F. Imaging the Separation Distance between the Attached Bacterial Cells and the Surface with a Total Internal Reflection Dark-Field Microscope. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8860-8866. [PMID: 31194567 DOI: 10.1021/acs.langmuir.9b01378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The attachment of bacterial cells to a surface is implicated in the formation of biofilms. Although the surface-related behaviors in this process, such as single cell motility and surface sensing, have been investigated intensively, the precise information of separation distance between the attached cells and the surface has remained unclear. Here, we set a prism-based total internal reflection dark-field microscope (p-TIRDFM) combined with the microfluidic method to image the separation distance of single attached cells. We directly observed that bacterial cells attached to the surface with one nearest touchpoint, and it gradually changed to two touchpoints, respectively, for the two offspring with the cell division. We first monitored the fluctuation of the relative distance on nanometer scale when cells twitch on a surface and further established the relationship between the twitching velocity and the separation distance. The results indicated that the moving cells are a considerable distance apart from the surface and the separation distance fluctuated more widely than immobile cells.
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31
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Feng L, Watanabe H, Molino P, Wallace GG, Phung SL, Uchihashi T, Higgins MJ. Dynamics of Inter-Molecular Interactions Between Single Aβ42 Oligomeric and Aggregate Species by High-Speed Atomic Force Microscopy. J Mol Biol 2019; 431:2687-2699. [DOI: 10.1016/j.jmb.2019.04.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 01/29/2023]
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32
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Liu L, Wu S, Pang H, Hu X, Hu X. High-speed atomic force microscope with a combined tip-sample scanning architecture. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:063707. [PMID: 31255009 DOI: 10.1063/1.5089534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
A high-speed atomic force microscope (HS-AFM) based on a tip-sample combined scanning architecture is presented. In this system, the X-scanner, which is separated from the AFM head, carries the sample and scans along the fast-axis. The Y and Z scanners integrated in the AFM head oscillate an ultrashort cantilever probe and scan in the other two dimensions. The optical beam deflection method is improved to enable the laser to track the probe over a wide scan range. A novel probe holder realizes easy exchange and alignment of the probe. Due to the separation of the X and Y scanners, both appear with better dynamic performance and carrying capacity. Experiments show that the HS-AFM established in this work can achieve a line rate of up to 100 Hz with the basic proportional-integral-derivative control algorithm and linear driving. The permissible sample size and mass can be as large as several centimeters and above 40 g.
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Sen Wu
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Hai Pang
- School of Science, Tianjin University, Tianjin 300072, China
| | - Xiaodong Hu
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Xiaotang Hu
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China
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33
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Strahlendorff T, Dai G, Bergmann D, Tutsch R. Tip wear and tip breakage in high-speed atomic force microscopes. Ultramicroscopy 2019; 201:28-37. [PMID: 30925297 DOI: 10.1016/j.ultramic.2019.03.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 02/12/2019] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
Abstract
Tip abrasion is a critical issue particularly for high-speed atomic force microscopy (AFM). In this paper, a quantitative investigation on the tip abrasion of diamond-like-carbon (DLC) coated tips in a high-speed metrological large range AFM device has been detailed. Wear tests are conducted on four different surfaces made of silicon, niobium, aluminum and steel. During the tests, different scanning speeds up to 1 mm/s and different vertical load forces up to approximately 33.2 nN are applied. Various tip characterization techniques such as scanning electron microscopy (SEM) and AFM tip characterizers have been jointly applied to measure the tip form change precisely. The experimental results show that tip form changes abruptly rather than progressively, particularly when structures with steep sidewalls were measured. This result indicates the increased tip breakage risk in high-speed AFM measurements. To understand the mechanism of tip breakage, tip-sample interaction is modelled, simulated and experimentally verified. The results indicate that the tip-sample interaction force increases dramatically in measurement scenarios of steep surfaces.
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Affiliation(s)
- Timo Strahlendorff
- Technische Universität Braunschweig, Institut für Produktionsmesstechnik, 38106 Braunschweig, Germany
| | - Gaoliang Dai
- Physikalisch-Technische Bundesanstalt (PTB), 38116 Braunschweig, Germany.
| | - Detlef Bergmann
- Physikalisch-Technische Bundesanstalt (PTB), 38116 Braunschweig, Germany
| | - Rainer Tutsch
- Technische Universität Braunschweig, Institut für Produktionsmesstechnik, 38106 Braunschweig, Germany
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34
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Heath GR, Scheuring S. Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and transporters. Curr Opin Struct Biol 2019; 57:93-102. [PMID: 30878714 DOI: 10.1016/j.sbi.2019.02.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023]
Abstract
Recent advances in high-speed atomic force microscopy (HS-AFM) have made it possible to study the conformational dynamics of single unlabeled transmembrane channels and transporters. Improving environmental control with the integration of a non-disturbing buffer exchange system, which in turn allows the gradual change of conditions during HS-AFM operation, has provided a breakthrough toward the performance of structural titration experiments. Further advancements in temporal resolution with the use of line scanning and height spectroscopy techniques show how high-speed atomic force microscopy can measure millisecond to microsecond dynamics, pushing this method beyond current spatial and temporal limits offered by less direct techniques.
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Affiliation(s)
- George R Heath
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065, USA
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065, USA.
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35
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Gupta P, Piyush P, Sriramshankar R, Jayanth GR. A high speed X-Y nanopositioner with integrated optical motion sensing. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:035002. [PMID: 30927770 DOI: 10.1063/1.5055715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 02/09/2019] [Indexed: 06/09/2023]
Abstract
High speed in-plane (X-Y) nanopositioners are of central importance in scanning probe microscopy for performing fast imaging and manipulation. Reducing the size of the nanopositioning stage improves the response speed of the positioner but also introduces challenges in integration of conventional motion sensors. This paper presents the design and development of a novel high speed flexure-guided, piezo-electrically actuated nanopositioner with integrated optical beam deflection-based motion sensing. The sensing strategy eliminates spatial constraints even for small stages. A simple lumped-parameter model is proposed for the nanopositioner. Subsequently, the model is used to design and fabricate the nanopositioner. The measurement system is integrated with the nanopositioning stage and is employed to characterize the quasi-static and dynamic response of the stage. Finally, the in-plane motion measurements are employed to control the stage when it is commanded to track both slow- and fast-varying position signals. In both cases, the use of control is shown to significantly improve the tracking accuracy.
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Affiliation(s)
- Priyanka Gupta
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India
| | - P Piyush
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India
| | - R Sriramshankar
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India
| | - G R Jayanth
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India
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36
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Characterization and enhanced antioxidant activity of the inclusion complexes of baicalin with p-sulfonatocalix[n]arenes. J INCL PHENOM MACRO 2019. [DOI: 10.1007/s10847-019-00887-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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Fukuma T, Garcia R. Atomic- and Molecular-Resolution Mapping of Solid-Liquid Interfaces by 3D Atomic Force Microscopy. ACS NANO 2018; 12:11785-11797. [PMID: 30422619 DOI: 10.1021/acsnano.8b07216] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hydration layers are ubiquitous in life and technology. Hence, interfacial aqueous layers have a central role in a wide range of phenomena from materials science to molecular and cell biology. A complete understanding of those processes requires, among other things, the development of very-sensitive and high-resolution instruments. Three-dimensional atomic force microscopy (3D-AFM) represents the latest and most successful attempt to generate atomically resolved three-dimensional images of solid-liquid interfaces. This review provides an overview of the 3D-AFM operating principles and its underlying physics. We illustrate and explain the capability of the instrument to resolve atomic defects on crystalline surfaces immersed in liquid. We also illustrate some of its applications to imaging the hydration structures on DNA or proteins. In the last section, we discuss some perspectives on emerging applications in materials science and molecular biology.
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Affiliation(s)
- Takeshi Fukuma
- Nano Life Science Institute (WPI-NanoLSI) , Kanazawa University , Kanazawa 920-1192 , Japan
| | - Ricardo Garcia
- Materials Science Factory , Instituto de Ciencia de Materiales de Madrid (ICMM) , 28049 Madrid , Spain
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38
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Evans CT, Payton O, Picco L, Allen MJ. Algal Viruses: The (Atomic) Shape of Things to Come. Viruses 2018; 10:E490. [PMID: 30213102 PMCID: PMC6165301 DOI: 10.3390/v10090490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 01/15/2023] Open
Abstract
Visualization of algal viruses has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. However, the high temporal (ms) and spatial resolution (nm) required, combined with the need to operate in physiologically relevant conditions presents a significant challenge. Here we present a short history of virus structure study and its relation to algal viruses and highlight current work, concentrating on electron microscopy and atomic force microscopy, towards the direct observation of individual algae⁻virus interactions. Finally, we make predictions towards future algal virus study direction with particular focus on the exciting opportunities offered by modern high-speed atomic force microscopy methods and instrumentation.
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Affiliation(s)
- Christopher T Evans
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK.
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
| | - Oliver Payton
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
| | - Loren Picco
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Michael J Allen
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK.
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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39
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刘 林, 魏 余, 刘 文, 孙 彤, 王 凯, 汪 颖, 李 宾. [Progress in the applications of high-speed atomic force microscopy in cell biology]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:931-937. [PMID: 30187879 PMCID: PMC6744042 DOI: 10.3969/j.issn.1673-4254.2018.08.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Indexed: 12/24/2022]
Abstract
Without losing its high resolution, high-speed atomic force microscope (HS-AFM) represents a perfect combinationof scanning speed and precision and allows real-time and in situ observation of the dynamic processes in a biological system atboth the cellular and molecular levels. By combining the extremely high temporal resolution with the spatial resolution andcoupling with other advanced technologies, HS-AFM shows promising prospects for applications in life sciences such as cellbiology. In this review, we summarize the latest progress of HS-AFM in the field of cell biology, and discuss the impact ofenvironmental factors on conformation dynamics of DNA, the binding processes between DNA and protein, the domainchanges of membrane proteins, motility of myosin, and surface structure changes of living cells.
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Affiliation(s)
- 林 刘
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 余辉 魏
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - 文静 刘
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 彤 孙
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 凯喆 王
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 颖 汪
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - 宾 李
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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40
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Heath GR, Harrison PL, Strong PN, Evans SD, Miller K. Visualization of diffusion limited antimicrobial peptide attack on supported lipid membranes. SOFT MATTER 2018; 14:6146-6154. [PMID: 29999090 DOI: 10.1039/c8sm00707a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the mechanism of action of antimicrobial peptides (AMP) is fundamental to the development and design of peptide based antimicrobials. Utilizing fast-scan atomic force microscopy (AFM) we detail the attack of an AMP on both prototypical prokaryotic (DOPC:DOPG) and eukaryotic (DOPC:DOPE) model lipid membranes on the nanoscale and in real time. Previously shown to have a favourable therapeutic index, we study Smp43, an AMP with a helical-hinge-helical topology isolated from the venom of the North African scorpion Scorpio maurus palmatus. We observe the dynamic formation of highly branched defects being supported by 2D diffusion models and further experimental data from liposome leakage assays and quartz crystal microbalance-dissipation (QCM-D) analysis, we propose that Smp43 disrupts these membranes via a common mechanism, which we have termed 'diffusion limited disruption' that encompasses elements of both the carpet model and the expanding pore mechanism.
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Affiliation(s)
- George R Heath
- Department of Physics and Astronomy, Leeds University, Leeds, LS2 9JT, UK.
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41
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Han G, Lin B. Optimal sampling and reconstruction of undersampled atomic force microscope images using compressive sensing. Ultramicroscopy 2018; 189:85-94. [DOI: 10.1016/j.ultramic.2018.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 02/05/2018] [Accepted: 03/26/2018] [Indexed: 11/25/2022]
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42
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Bhat SV, Sultana T, Körnig A, McGrath S, Shahina Z, Dahms TES. Correlative atomic force microscopy quantitative imaging-laser scanning confocal microscopy quantifies the impact of stressors on live cells in real-time. Sci Rep 2018; 8:8305. [PMID: 29844489 PMCID: PMC5973941 DOI: 10.1038/s41598-018-26433-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/04/2018] [Indexed: 11/14/2022] Open
Abstract
There is an urgent need to assess the effect of anthropogenic chemicals on model cells prior to their release, helping to predict their potential impact on the environment and human health. Laser scanning confocal microscopy (LSCM) and atomic force microscopy (AFM) have each provided an abundance of information on cell physiology. In addition to determining surface architecture, AFM in quantitative imaging (QI) mode probes surface biochemistry and cellular mechanics using minimal applied force, while LSCM offers a window into the cell for imaging fluorescently tagged macromolecules. Correlative AFM-LSCM produces complimentary information on different cellular characteristics for a comprehensive picture of cellular behaviour. We present a correlative AFM-QI-LSCM assay for the simultaneous real-time imaging of living cells in situ, producing multiplexed data on cell morphology and mechanics, surface adhesion and ultrastructure, and real-time localization of multiple fluorescently tagged macromolecules. To demonstrate the broad applicability of this method for disparate cell types, we show altered surface properties, internal molecular arrangement and oxidative stress in model bacterial, fungal and human cells exposed to 2,4-dichlorophenoxyacetic acid. AFM-QI-LSCM is broadly applicable to a variety of cell types and can be used to assess the impact of any multitude of contaminants, alone or in combination.
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Affiliation(s)
- Supriya V Bhat
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Taranum Sultana
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - André Körnig
- JPK Instruments, JPK Instruments AG, Colditzstr. 34-36, 12099, Berlin, Germany
| | - Seamus McGrath
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Zinnat Shahina
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada.
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43
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Hartman B, Andersson SB. Feature Tracking for High Speed AFM Imaging of Biopolymers. Int J Mol Sci 2018; 19:ijms19041044. [PMID: 29614750 PMCID: PMC5979492 DOI: 10.3390/ijms19041044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 03/15/2018] [Accepted: 03/28/2018] [Indexed: 11/16/2022] Open
Abstract
The scanning speed of atomic force microscopes continues to advance with some current commercial microscopes achieving on the order of one frame per second and at least one reaching 10 frames per second. Despite the success of these instruments, even higher frame rates are needed with scan ranges larger than are currently achievable. Moreover, there is a significant installed base of slower instruments that would benefit from algorithmic approaches to increasing their frame rate without requiring significant hardware modifications. In this paper, we present an experimental demonstration of high speed scanning on an existing, non-high speed instrument, through the use of a feedback-based, feature-tracking algorithm that reduces imaging time by focusing on features of interest to reduce the total imaging area. Experiments on both circular and square gratings, as well as silicon steps and DNA strands show a reduction in imaging time by a factor of 3-12 over raster scanning, depending on the parameters chosen.
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Affiliation(s)
- Brett Hartman
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA.
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA.
- Division of Systems Engineering, Boston University, Boston, MA 02215, USA.
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44
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Tao J, Nielsen MH, De Yoreo JJ. Nucleation and phase transformation pathways in electrolyte solutions investigated by in situ microscopy techniques. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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45
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Nautiyal P, Alam F, Balani K, Agarwal A. The Role of Nanomechanics in Healthcare. Adv Healthc Mater 2018; 7. [PMID: 29193838 DOI: 10.1002/adhm.201700793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/18/2017] [Indexed: 12/21/2022]
Abstract
Nanomechanics has played a vital role in pushing our capability to detect, probe, and manipulate the biological species, such as proteins, cells, and tissues, paving way to a deeper knowledge and superior strategies for healthcare. Nanomechanical characterization techniques, such as atomic force microscopy, nanoindentation, nanotribology, optical tweezers, and other hybrid techniques have been utilized to understand the mechanics and kinetics of biospecies. Investigation of the mechanics of cells and tissues has provided critical information about mechanical characteristics of host body environments. This information has been utilized for developing biomimetic materials and structures for tissue engineering and artificial implants. This review summarizes nanomechanical characterization techniques and their potential applications in healthcare research. The principles and examples of label-free detection of cancers and myocardial infarction by nanomechanical cantilevers are discussed. The vital importance of nanomechanics in regenerative medicine is highlighted from the perspective of material selection and design for developing biocompatible scaffolds. This review interconnects the advancements made in fundamental materials science research and biomedical technology, and therefore provides scientific insight that is of common interest to the researchers working in different disciplines of healthcare science and technology.
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Affiliation(s)
- Pranjal Nautiyal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
| | - Fahad Alam
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Kantesh Balani
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Arvind Agarwal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
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46
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Marsh BP, Chada N, Sanganna Gari RR, Sigdel KP, King GM. The Hessian Blob Algorithm: Precise Particle Detection in Atomic Force Microscopy Imagery. Sci Rep 2018; 8:978. [PMID: 29343783 PMCID: PMC5772630 DOI: 10.1038/s41598-018-19379-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/29/2017] [Indexed: 11/09/2022] Open
Abstract
Imaging by atomic force microscopy (AFM) offers high-resolution descriptions of many biological systems; however, regardless of resolution, conclusions drawn from AFM images are only as robust as the analysis leading to those conclusions. Vital to the analysis of biomolecules in AFM imagery is the initial detection of individual particles from large-scale images. Threshold and watershed algorithms are conventional for automatic particle detection but demand manual image preprocessing and produce particle boundaries which deform as a function of user-defined parameters, producing imprecise results subject to bias. Here, we introduce the Hessian blob to address these shortcomings. Combining a scale-space framework with measures of local image curvature, the Hessian blob formally defines particle centers and their boundaries, both to subpixel precision. Resulting particle boundaries are independent of user defined parameters, with no image preprocessing required. We demonstrate through direct comparison that the Hessian blob algorithm more accurately detects biomolecules than conventional AFM particle detection techniques. Furthermore, the algorithm proves largely insensitive to common imaging artifacts and noise, delivering a stable framework for particle analysis in AFM.
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Affiliation(s)
- Brendan P Marsh
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America.,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 OWA, United Kingdom
| | - Nagaraju Chada
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America
| | - Raghavendar Reddy Sanganna Gari
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America.,School of Medicine, University of Virginia, Charlottesville, Virginia, 22908, United States of America
| | - Krishna P Sigdel
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, United States of America. .,Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, United States of America.
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47
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Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields. For instance in biological sciences, where it is paramount to investigate structures at the single particle level. Often two-dimensional images are not sufficient and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. By including new approaches such as high-speed AFM (HS-AFM) we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
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Affiliation(s)
- Melissa C Piontek
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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48
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Zuttion F, Redondo-Morata L, Marchesi A, Casuso I. High-Resolution and High-Speed Atomic Force Microscope Imaging. Methods Mol Biol 2018; 1814:181-200. [PMID: 29956233 DOI: 10.1007/978-1-4939-8591-3_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The advent of high-speed atomic force microscopy (HS-AFM) over the recent years has opened up new horizons for the study of structure, function and dynamics of biological molecules. HS-AFM is capable of 1000 times faster imaging than conventional AFM. This circumstance uniquely enables the observation of the dynamics of all the molecules present in the imaging area. Over the last 10 years, the HS-AFM has gone from a prototype-state technology that only a few labs in the world had access to (including ours) to an established commercialized technology that is present in tens of labs around the world. In this protocol chapter we share with the readers our practical know-how on high resolution HS-AFM imaging.
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Affiliation(s)
- Francesca Zuttion
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 13009, Marseille, France
| | - Lorena Redondo-Morata
- Inserm U1019, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Arin Marchesi
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 13009, Marseille, France
| | - Ignacio Casuso
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 13009, Marseille, France.
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49
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Harcombe DM, Ruppert MG, Ragazzon MRP, Fleming AJ. Lyapunov estimation for high-speed demodulation in multifrequency atomic force microscopy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2018. [PMID: 29515961 PMCID: PMC5815288 DOI: 10.3762/bjnano.9.47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
An important issue in the emerging field of multifrequency atomic force microscopy (MF-AFM) is the accurate and fast demodulation of the cantilever-tip deflection signal. As this signal consists of multiple frequency components and noise processes, a lock-in amplifier is typically employed for its narrowband response. However, this demodulator suffers inherent bandwidth limitations as high-frequency mixing products must be filtered out and several must be operated in parallel. Many MF-AFM methods require amplitude and phase demodulation at multiple frequencies of interest, enabling both z-axis feedback and phase contrast imaging to be achieved. This article proposes a model-based multifrequency Lyapunov filter implemented on a field-programmable gate array (FPGA) for high-speed MF-AFM demodulation. System descriptions and simulations are verified by experimental results demonstrating high tracking bandwidths, strong off-mode rejection and minor sensitivity to cross-coupling effects. Additionally, a five-frequency system operating at 3.5 MHz is implemented for higher harmonic amplitude and phase imaging up to 1 MHz.
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Affiliation(s)
- David M Harcombe
- School of Electrical Engineering and Computing, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Michael G Ruppert
- School of Electrical Engineering and Computing, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Michael R P Ragazzon
- Department of Engineering Cybernetics, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Andrew J Fleming
- School of Electrical Engineering and Computing, The University of Newcastle, Callaghan, NSW, 2308, Australia
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50
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Wessels WA, Bollmann TRJ, Post D, Koster G, Rijnders G. Imaging pulsed laser deposition oxide growth by in situ atomic force microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:123902. [PMID: 29289154 DOI: 10.1063/1.5004567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To visualize the topography of thin oxide films during growth, thereby enabling to study its growth behavior quasi real-time, we have designed and integrated an atomic force microscope (AFM) in a pulsed laser deposition (PLD) vacuum setup. The AFM scanner and PLD target are integrated in a single support frame, combined with a fast sample transfer method, such that in situ microscopy can be utilized after subsequent deposition pulses. The in situ microscope can be operated from room temperature up to 700 °C and at (process) pressures ranging from the vacuum base pressure of 10-6 mbar up to 1 mbar, typical PLD conditions for the growth of oxide films. The performance of this instrument is demonstrated by resolving unit cell height surface steps and surface topography under typical oxide PLD growth conditions.
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Affiliation(s)
- W A Wessels
- Inorganic Materials Science, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, NL-7500AE Enschede, The Netherlands
| | - T R J Bollmann
- Inorganic Materials Science, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, NL-7500AE Enschede, The Netherlands
| | - D Post
- Inorganic Materials Science, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, NL-7500AE Enschede, The Netherlands
| | - G Koster
- Inorganic Materials Science, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, NL-7500AE Enschede, The Netherlands
| | - G Rijnders
- Inorganic Materials Science, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, NL-7500AE Enschede, The Netherlands
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